Mercurial > repos > davidvanzessen > argalaxy_tools

comparison imgt_loader/imgt_loader.r @ 28:798b62942b4b draft

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author davidvanzessen
date Wed, 01 Mar 2017 10:41:30 -0500
parents 9185c3dfc679
children 3a76faa53c59
comparison
equal deleted inserted replaced
27:b539aeb75980 28:798b62942b4b
2 2
3 summ.file = args[1] 3 summ.file = args[1]
4 sequences.file = args[2] 4 sequences.file = args[2]
5 aa.file = args[3] 5 aa.file = args[3]
6 junction.file = args[4] 6 junction.file = args[4]
7 out.file = args[5] 7 gapped.aa.file = args[5]
8 out.file = args[6]
8 9
9 summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T) 10 summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T)
10 sequences = read.table(sequences.file, sep="\t", header=T, quote="", fill=T) 11 sequences = read.table(sequences.file, sep="\t", header=T, quote="", fill=T)
11 aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T) 12 aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T)
13 gapped.aa = read.table(gapped.aa.file, sep="\t", header=T, quote="", fill=T)
12 junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T) 14 junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T)
13 15
14 old_summary_columns=c('Sequence.ID','JUNCTION.frame','V.GENE.and.allele','D.GENE.and.allele','J.GENE.and.allele','CDR1.IMGT.length','CDR2.IMGT.length','CDR3.IMGT.length','Orientation') 16 old_summary_columns=c('Sequence.ID','JUNCTION.frame','V.GENE.and.allele','D.GENE.and.allele','J.GENE.and.allele','CDR1.IMGT.length','CDR2.IMGT.length','CDR3.IMGT.length','Orientation')
15 old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT') 17 old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT')
16 old_junction_columns=c('JUNCTION') 18 old_junction_columns=c('JUNCTION')
30 out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"] 32 out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"]
31 33
32 out[,"CDR3.Seq"] = aa[,"CDR3.IMGT"] 34 out[,"CDR3.Seq"] = aa[,"CDR3.IMGT"]
33 out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"] 35 out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"]
34 36
35 out[,"CDR3.Seq.DNA"] = sequences[,"CDR3.IMGT"] 37 out[,"CDR3.Seq.DNA"] = gapped.aa[,"CDR3.IMGT"]
36 out[,"CDR3.Length.DNA"] = nchar(as.character(sequences[,"CDR3.IMGT"])) 38 out[,"CDR3.Length.DNA"] = nchar(as.character(out[,"CDR3.Seq.DNA"]))
37 out[,"Strand"] = summ[,"Orientation"] 39 out[,"Strand"] = summ[,"Orientation"]
38 out[,"CDR3.Found.How"] = "a" 40 out[,"CDR3.Found.How"] = "a"
39 41
40 out[,added_summary_columns] = summ[,added_summary_columns] 42 out[,added_summary_columns] = summ[,added_summary_columns]
41 43